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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaccaacattttaaattctgcaagcataaagagaaatattactcagtgtcgcagaaaatttattgttcttttccaaaatttactcagtcaggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGACAATACAGTCAGAGATACCTGTATTTGTACAACCAGAAGCAAGTAACAT

Basic information

species Zea mays
transcript GRMZM5G875776_T01
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211337942|gb|FL007017.1|FL007017
EST:     AATAATCATTGTGCATATTCGAGACATGGAAAATGCAG                         GGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGA
genomic: AATAATCATTGTGCATATTCGAGACATGGAAAATGCAGgtgcaccaac ... ggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGA
EST: gi|71429002|gb|DR810052.1|DR810052
EST:     AGATGATATAACAATAATCATTGTGCATATTCGAGACATGGAAAATGCAG                         GGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGA
genomic: AGATGATATAACAATAATCATTGTGCATATTCGAGACATGGAAAATGCAGgtgcaccaac ... ggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 38 (upstream exon), 44 (downstream exon)
Score: 13

CATACAAACTATGGCTTGAGCATGAAAACAGGACAGATGATATAACAATAATCATTGTGCATATTCGAGACATGGAAAATGCAGgtgcaccaac ... ggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGACAATACAGTCAGAGATACCTGTATTTGTACAACCAGAAGCAAGTAACAT


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 4

CATACAAACTATGGCTTGAGCATGAAAACAGGACAGATGATATAACAATAATCATTGTGCATATTCGAGACATGGAAAATGCAGgtgcaccaac ... ggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGACAATACAGTCAGAGATACCTGTATTTGTACAACCAGAAGCAAGTAACAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 8

CATACAAACTATGGCTTGAGCATGAAAACAGGACAGATGATATAACAATAATCATTGTGCATATTCGAGACATGGAAAATGCAGgtgcaccaac ... ggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGACAATACAGTCAGAGATACCTGTATTTGTACAACCAGAAGCAAGTAACAT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 11

CATACAAACTATGGCTTGAGCATGAAAACAGGACAGATGATATAACAATAATCATTGTGCATATTCGAGACATGGAAAATGCAGgtgcaccaac ... ggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGACAATACAGTCAGAGATACCTGTATTTGTACAACCAGAAGCAAGTAACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcgcagaaaatttattgttcttttccaaaatttactcagtcaggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGACAATACAGTCAGAGATACCTGTATTTGTACAACCAGAAGCAAGTAACAT
         aaaatttattgttctt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaccaacattttaaattctgcaagcataaagagaaatattactcagtgtcgcagaaaatttattgttcttttccaaaatttactcagtcaggtcctgcagGGAGTGACAAAGCGGACTATGGTAGCATCGGAGCATCAATAGCTGGGCAGACAATACAGTCAGAGATACCTGTATTTGTACAACCAGAAGCAAGTAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG